It's the first day of Tadayasu and Kei's university life. Tadayasu shows off his ability to Professor Itsuki and Haruka. The talent show is cut short when Tadayasu spots fructivorans in the air.

Hazuki Oikawa is introduced. She comes to Kaoru and Takuma's dorm room and kills the bacteria they were planning to cultivate. Everyone is summoned back to the lab where Professor Itsuki and Haruka show them how to make sake for educational purposes.

The first years are invited on a tour around the campus and a picnic. Tadayasu spots harmful bacteria in the food and saves everyone from E. coli food poisoning.

Tadayasu becomes disgusted when he sees a man covered in microbes. Professor Itsuki asks everyone to buy liquor at Hiyoshi Liquor Store near the school. Tadayasu discovers the owner is the microbe monster who brews delicious sake.

Aoi Mutō returns from a long trip bringing fermented meat. She also brings Vibrio parahaemolyticus, El Tor, Shigella dysenteriae, Salmonella enterica and Plesiomonas shigelloides. After getting disinfected, Aoi brings Tadayasu to the UFO club room where all the members are sick and unintentionally breeding new forms of influenza with pigs and chickens.

The spring agricultural festival has started, and that means that during this time, the campus is closed and students have to exchange real money for school money, but when the festival ends the school money is worthless and cannot be exchanged back for real money. There are also many special rules related to the event that students have to find out on their own.

It is the third day of the spring agricultural festival, and the students are forming a resistance in order to end the festival. At 4:00 PM, the students charge towards the front gate to engage in a battle, and during this time, Kaoru, Takuma, and Tadayasu work together to take down the robot in front of the gate and effectively end the festival. In return, they get 100,000 school yen which they use to get Professor Itsuki's aphrodisiac, they try to get one of the girls to take one but Haruka foils their plan by using all of them on herself, seemingly immune to their effects. Oikawa and Mutō get some from the professor themselves and sleep with each other as a result.

Professor Itsuki holds a celebration for Kaoru and Takuma getting part-time jobs, and during this party introduces everyone to the foul-smelling surströmming. Later, Haruka is summoned to a private dinner with her father and fiancé, but gets Kaoru and Takuma, who had actually been working at the restaurant before getting fired by Haruka minutes before, to think of something to get her out of the dinner. They call Tadayasu who brings a can of surströmming; once the can is opened, Kaoru and Takuma take Haruka out in the confusion and go to a bar.

After not seeing Kei for a while, Tadayasu discovers that he is working at Hiyoshi's liquor store, and on top of that is cross-dressing as a Gothic Lolita. Unexpectedly, Kei kisses Tadayasu, and afterwards Tadayasu discovers that he cannot see microbes anymore. This has happened before, but Haruka finds out and confronts him about the loss of his ability.

Haruka thinks that without his ability to see microbes, there is not much reason for him to be at the university anymore, though Kaoru and Takuma stick up for him. Tadayasu seeks advice from Kei, and in the process finds out that despite Kei getting mad in the past for being called feminine, he decided that deep down he was not being entirely honest with himself about his gender identity. Haruka reconciles with Tadayasu later, and at that time Tadayasu regains the ability to see microbes once more.